Multiple-sample microfluidic chip for DNA analysis

ABSTRACT

Aspects of the disclosure provide a microfluidic chip. The microfluidic chip includes a first domain configured for polymerase chain reaction (PCR) amplification of DNA fragments, and a second domain for electrophoretic separation. The first domain includes at least a first reaction reservoir designated for PCR amplification based on a first sample, and a second reaction reservoir designated for PCR amplification based on a second sample. The second domain includes at least a first separation unit coupled to the first reaction reservoir to received first amplified DNA fragments based on the first sample, and a second separation unit coupled to the second reaction reservoir to received second amplified DNA fragments based on the second sample. The first separation unit is configured to perform electrophoretic separation for the first amplified DNA fragments, and the second separation unit is configured to perform electrophoretic separation for the second amplified DNA fragments.

INCORPORATION BY REFERENCE

This application claims the benefit of U.S. Provisional Applications No.61/213,405, “Fast Sample to Answer DNA Analyzer (AnalyticalMicrodevice)” filed on Jun. 4, 2009, No. 61/213,406, “Optical Approachfor Microfluidic DNA Electrophoresis Detection” filed on Jun. 4, 2009,and No. 61/213,404, “Multiple Sample, Integrated Microfluidic Chip forDNA Analysis” filed on Jun. 4, 2009, which are incorporated herein byreference in their entirety.

BACKGROUND

DNA is recognized as the “ultimate biometric” for human identification.DNA analysis can provide evidence for solving forensic and medicalcases, such as in areas of criminal justice, identifications of humanremains, paternity testing, pathogen detection, disease detection, andthe like.

SUMMARY

Aspects of the disclosure can provide a microfluidic chip. Themicrofluidic chip includes a first domain configured for polymerasechain reaction (PCR) amplification of DNA fragments, and a second domainfor electrophoretic separation. The first domain includes at least afirst reaction reservoir designated for PCR amplification based on afirst sample, and a second reaction reservoir designated for PCRamplification based on a second sample. The second domain includes atleast a first separation unit coupled to the first reaction reservoir toreceived first amplified DNA fragments based on the first sample, and asecond separation unit coupled to the second reaction reservoir toreceived second amplified DNA fragments based on the second sample. Thefirst separation unit is configured to perform electrophoreticseparation for the first amplified DNA fragments, and the secondseparation unit is configured to perform electrophoretic separation forthe second amplified DNA fragments. It is noted that the microfluidicchip can include other domains, such as purification domain, post-PCRdomain, and the like, configured for multiple samples.

Further, the microfluidic chip includes first inlets configured to inputa first template DNA extracted from the first sample and first reagentsfor PCR amplification into the first reaction reservoir, and secondinlets configured to input a second template DNA extracted from thesecond sample and second reagents for PCR amplification into the secondreaction reservoir.

In an embodiment, the first separation unit includes a first separationchannel configured to separate the first amplified DNA fragments byelectrophoretic separation, and a first injection channel configured toinject the first amplified DNA fragments into the first separationchannel by electro-kinetic injection. Similarly, the second separationunit includes a second separation channel configured to separate thesecond amplified DNA fragments by electrophoretic separation, and asecond injection channel configured to inject the second amplified DNAfragments into the second separation channel by electro-kineticinjection.

Further, the first separation unit includes first electrode reservoirsconfigured to apply electric fields for the electro-kinetic injectionand the electrophoretic separation in the first separation unit.Similarly, the second separation unit includes second electrodereservoirs configured to apply electric fields for the electro-kineticinjection and the electrophoretic separation. The first separation unitand the second separation unit can share at least one electrodereservoir.

In an embodiment, the first domain includes a thermal coupler reservoirconfigured for measuring a temperature within the first domain.

Further, the microfluidic chip includes a dilution domain. The dilutiondomain dilutes PCR mixtures received from the first domain and preparesthe PCR mixtures for electrophoretic separations in the second domain.In an example, the dilution domain includes a first dilution reservoirdesignated for diluting a first PCR mixture received from the firstreaction reservoir, and a second dilution reservoir designated fordiluting a second PCR mixture received from the second reactionreservoir. The first dilution reservoir dilutes the first PCR mixturewith a first dilutant according to a first ratio from 1:5 to 1:20, andthe second dilution reservoir dilutes the second PCR mixture with asecond dilutant according to a second ratio from 1:5 to 1:20.

Aspects of the disclosure can provide a cartridge. The cartridgeincludes a sample acceptor and the microfluidic chip coupled together.The sample acceptor is configured to respectively extract a firsttemplate DNA from a first sample and a second template DNA from a secondsample. The sample acceptor is configured to extract the first templateDNA or the second template DNA by at least one of a solid phaseextraction, and a liquid phase enzymatic DNA isolation. In anembodiment, the sample acceptor includes a first well having a firstliquid phase mixture to extract the first template DNA from the firstsample and a second well having a second liquid phase mixture to extractthe second template DNA from the second sample.

Further, the cartridge includes a reagent carrier configured to carryreagents for the PCR amplification, and solutions for theelectrophoretic separation.

Aspects of the disclosure can provide a method for multiple-sample DNAanalysis. The method includes inducing thermal cycles in a first domainof a microfluidic chip for PCR amplification of DNA fragments. The firstdomain includes at least a first reaction reservoir designated for PCRamplification based on a first sample, and a second reaction reservoirdesignated for PCR amplification based on a second sample. Further, themethod includes inducing liquid flow to respectively move firstamplified DNA fragments from the first reaction reservoir to a firstseparation unit in a second domain of the microfluidic chip, and secondamplified DNA fragments from the second reaction reservoir to a secondseparation unit in the second domain of the microfluidic chip. Then, themethod includes inducing electric fields in the first separation unit toseparate the first amplified DNA fragments by size, and inducingelectric fields in the second separation unit to separate the secondamplified DNA fragments by size. Further, the method includes detectingthe separated DNA fragments.

The method can also include extracting a first template DNA from thefirst sample, and extracting a second template DNA from the secondsample. In an embodiment, the method includes maintaining a temperatureto enable liquid phase enzymatic DNA isolation for extracting at leastone of the first template DNA and the second template DNA. Further, themethod includes injecting first reagents and the first template DNA intothe first reaction reservoir, and injecting second reagents and thesecond template DNA into the second reaction reservoir.

To detect the separated DNA fragments, the method can include emitting alaser beam, splitting the laser beam into a first laser beam and asecond laser beam, directing the first laser beam to a first separationchannel of the first separation unit to excite a first fluorescence fromfirst fluorescent labels attached to the first amplified DNA fragmentsand directing the second laser beam to a second separation channel ofthe second separation unit to excite a second fluorescence from secondfluorescent labels attached to the second amplified DNA fragments. Then,the method includes detecting the first fluorescence and the secondfluorescence.

To detect the first fluorescence and the second fluorescence, the methodcan include detecting the first fluorescence by a first detector, anddetecting the second fluorescence by a second detector. Alternatively,the method includes multiplexing the first fluorescence and the secondfluorescence, and detecting the multiplexed fluorescence by a detector.

In an embodiment, the microfluidic chip includes a dilution domain. Thedilution domain includes a first dilution reservoir and a seconddilution reservoir. Then, the method includes inducing liquid flow tomove a first PCR mixture having the first amplified DNA fragments fromthe first reaction reservoir to a first dilution reservoir, diluting thefirst PCR mixture with a first dilutant, inducing liquid flow to move asecond PCR mixture having the second amplified DNA fragments from thesecond reaction reservoir to a second dilution reservoir, and dilutingthe second PCR mixture with a second dilutant.

BRIEF DESCRIPTION OF THE DRAWINGS

Various exemplary embodiments of this disclosure will be described indetail with reference to the following figures, wherein like numeralsreference like elements, and wherein:

FIG. 1 shows a block diagram of an exemplary DNA analyzer according toan embodiment of the disclosure;

FIGS. 2A-2C show a swab example and elevation views of a samplecartridge example according to an embodiment of the disclosure;

FIG. 3 shows a schematic diagram of a microfluidic chip exampleaccording to an embodiment of the disclosure;

FIG. 4 shows an exemplary DNA analyzer according to an embodiment of thedisclosure;

FIG. 5 shows a schematic diagram of a multiple-sample microfluidic chipexample according to an embodiment of the disclosure;

FIG. 6 shows a block diagram of a detection module example formultiple-sample DNA analysis according to an embodiment of thedisclosure;

FIG. 7 shows a flow chart outlining an exemplary process for using a DNAanalyzer to perform multiple-sample DNA analysis according to anembodiment of the disclosure; and

FIG. 8 shows a flow chart outlining an exemplary process for a DNAanalyzer to perform multiple-sample DNA analysis according to anembodiment of the disclosure.

DETAILED DESCRIPTION OF EMBODIMENTS

FIG. 1 shows a block diagram of an exemplary DNA analyzer 100 accordingto an embodiment of the disclosure. The DNA analyzer 100 includes amicrofluidic chip module 110, a thermal module 120, a pressure module130, a high voltage module 140, a detection module 150, a power module160, a computing module 170, and a controller module 180. Additionally,the DNA analyzer 100 can include a magnetic module 190. These elementscan be coupled together as shown in FIG. 1.

The DNA analyzer 100 is capable of processing sample-to-answer DNAanalysis on an integrated single-chip. Thus, using the DNA analyzer 100to perform DNA analysis does not need substantial experience andknowledge of DNA processes. In an example, the appropriate procedures touse the DNA analyzer 100 to perform DNA analysis can be learned in anhour. Additionally, the integrated single-chip DNA analysis requires areduced volume of reagents, for example, in the order of a micro-liter.Further, the reduced volume of reagents can reduce thermal inputs forinducing thermal cycles in the DNA analysis, and thus reduce the timefor DNA analysis.

The microfluidic chip module 110 includes a microfluidic chip 111. Themicrofluidic chip 111 can be suitably coupled with other elements of theDNA analyzer 100 to perform integrated single-chip DNA analysis. In anexample, the microfluidic chip module 110 is implemented as a disposablecartridge, and a cartridge interface that can couple the disposablecartridge with other components of the DNA analyzer 100 that are notincluded as part of the disposable cartridge. The disposable cartridgeincludes the microfluidic chip 111 and a micro-to-macro interface. Themicro-to-macro interface couples the microfluidic chip 111 to macrostructures on the disposable cartridge. The disposable cartridge can beseparately stored, and can be installed in the DNA analyzer 100 at atime of DNA analysis. After the DNA analysis, the disposable cartridgecan be suitably thrown away.

The microfluidic chip 111 includes various domains that can be suitablyconfigured to enable the integrated single-chip DNA analysis. In anembodiment, DNA analysis generally includes a step of PCR amplification,and a step of electrophoretic separation. The microfluidic chip 111 caninclude a first domain 111 a for the PCR amplification and a seconddomain 111 b for the electrophoretic separation. In addition, themicrofluidic chip 111 can include other domains that are suitablyintegrated with the first domain 111 a and the second domain 111 b. Inan example, the microfluidic chip 111 includes a purification domainfluidically coupled with the first domain 111 a. The purification domaincan be used to extract and purify a template DNA. It is noted that anysuitable techniques, such as solid-phase extraction, liquid-phaseextraction, and the like, can be used to purify the template DNA in thepurification domain.

In another example, the microfluidic chip 111 includes a post-PCRclean-up/dilution domain that is fluidically coupled with the firstdomain 111 a and the second domain 111 b. The post-PCR clean-up/dilutiondomain can be used for any suitable process after the PCR amplificationand before the electrophoretic separation.

The first domain 111 a includes a reservoir configured for PCRamplification. In an embodiment, the first domain 111 a includesmultiple separated reservoirs to enable simultaneous PCR amplificationfor multiple DNA samples. The temperature at the first domain 111 a canbe controlled by the thermal module 120 to enable the PCR amplification.According to an embodiment of the disclosure, the PCR amplification onthe microfluidic chip 111 requires only a small volume of reagents, andthe PCR amplification can achieve rapid thermal cycling. In an example,the volume of reagents used for the PCR amplification can be in theorder of sub-micro-liter, and the time required for the PCRamplification can be under 20 minutes.

The second domain 111 b can include a plurality of micro channels. Theplurality of micro channels can be configured for electrophoreticseparation. More specifically, each micro channel can be filled with,for example, polymer sieving matrix. Further, an electric field can beinduced in the micro channel. Thus, when DNA fragments are injected inthe micro channel, the DNA fragments can migrate by force of theelectric field at different speeds based on the sizes of the DNAfragments.

Additionally, the second domain 111 b can be configured to facilitateDNA fragments detection in the DNA analysis. In an example, DNAfragments are tagged with fluorescent labels during PCR, before beinginjected in the micro channels. The fluorescent labels can emitfluorescence of pre-known wavelength when excited by a laser beam. Thesecond domain 111 b includes a detection window configured fordetection. The laser beam can be directed to pass through the detectionwindow to excite the fluorescent labels in the micro channels. Theemitted fluorescence can pass through the detection window to becollected and detected.

The microfluidic chip 111 can include additional structures tofacilitate the integrated single-chip DNA analysis. For example, themicrofluidic chip 111 can include microfluidic channels that can directDNA fragments from the first domain 111 a to the second domain 111 b.Through the microfluidic channels, the DNA fragments flow in a solutionfrom the first domain 111 a to the second domain 111 b. In addition, themicrofluidic chip 111 can include inlets for receiving reagents and thetemplate DNA. The microfluidic chip 111 can also include additionalreservoirs for additional processing steps, such as dilution, cleanup,and the like.

The microfluidic chip 111 can be constructed from any suitable material.In an example, the microfluidic chip 111 is constructed from glass. Inanother example, the microfluidic chip 111 is constructed from plasticor polymeric material.

In addition to the microfluidic chip 111, the disposable cartridge caninclude a sample acceptor and a reagent carrier. In an example, thesample acceptor accepts a swab used for taking DNA sample, such as fromsaliva, bloodstains, cigarettes, and the like. Further, the sampleacceptor extracts a template DNA from the swab. The sample acceptor canuse any suitable mechanism, such as solid-phase extraction, liquid-phaseextraction, and the like to obtain and/or purify the template DNA fromthe swab. In an embodiment, the sample acceptor uses a solid-phase DNAextraction method, such as silica beads based DNA extraction.

In another embodiment, the sample acceptor uses a liquid-phase DNAextraction method. The liquid-phase DNA extraction method can simplifythe purification and extraction process, and reduce a total cost of theDNA analyzer 100. In an example, the sample acceptor uses an enzymaticDNA-isolation method to extract and purify the template DNA. Theenzymatic DNA-isolation method can achieve liquid phase purificationwithout a need of centrifugation. In addition, the sample acceptor canbe suitably designed to maintain sample integrity.

More specifically, the sample acceptor can include a plurality ofseparated wells for taking swabs, for example. Thus, the DNA analysiscan simultaneously process multiple DNA samples. Each well includes aliquid phase mixture that is sealed by a membrane at a bottom portion ofthe well. The liquid phase mixture can conduct enzymatic digestion ofall proteins and other cellular interferences, with the exception ofDNA. For example, the liquid phase mixture can include thermostableproteinases from thermophilic Bacillus species, such as disclosed inU.S. Patent Application Publication No. 2004/0197788, which isincorporated herein by reference in its entirety. Thus, the liquid phasemixture can perform DNA extraction and purification when a swab isimmersed in the liquid phase mixture. The liquid phase method canachieve comparable DNA quality to other methodologies in both DNAconcentration and purity. In an example, a final DNA concentration bythe liquid phase method is in a range of 0.5-2 ng/μL.

Further, using the liquid phase extraction method instead of the silicasolid phase method can reduce the overall hydraulic pressure requirementto induce solution flow through the microfluidic chip 111. In anembodiment, the liquid phase extraction can enable a valveless designfor the microfluidic chip 111. Thus, the liquid phase extraction cansimplify the DNA analyzer 100 and simplify the manufacturing and testingsteps in association with the solid-phase extraction.

Before taking DNA sample, a swab can be sealed in a hard case to avoidcontamination. The swab can be attached to a seal cap that can seal thehard case. The swab can be identified by various mechanisms. In anexample, a barcode label is attached to the hard case to identify theswab. In another example, the seal cap has a radio frequencyidentification (RFID) tag implanted. The RFID tag can identify the swabattached to the seal cap throughout the process. After the swab is usedto take DNA sample, the swab can be placed in one of the plurality ofseparated wells, and can be sealed in the well, for example, by the sealcap attached to the sampled swab. In an embodiment, the seal cap is astepped seal cap that can seal the well in a first step, and a secondstep. When the seal cap seals the well in the first step, the swab doesnot puncture the membrane. When the seal cap seals the well in thesecond step, the swab punctures the membrane and is immersed in theliquid phase mixture. The liquid phase mixture can then extract templateDNA from the swab.

The reagent carrier can house a plurality of reagents for DNA analysis,such as reagents for polymerase chain reaction (PCR) amplification,solutions for electrophoretic separation, and the like. In an STR typingexample, the reagent carrier houses reagents for multiplexed STRamplification. The reagents can perform multiplexed STR amplificationand can use multiple fluorescent dyes to label STR alleles. The reagentscan be commercially available reagent kits or can be tailored to themicro-scale chip environment to further facilitate the integratedsingle-chip DNA analysis.

In addition, the reagent carrier houses solutions that are suitable forelectrophoretic separation in the micro-scale chip environment. Forexample, the reagent carrier houses a coating solution, such aspoly-N-hydroxyethylacrylamide, and the like. The coating solution can beused to coat micro channel walls prior to the separation to reduceelectro osmotic flow and enable single base pair resolution of amplifiedDNA fragments. In another example, the reagent carrier houses a dilutionsolution, such as water and/or Formamide, and the like. The dilutionsolution can be used to reduce the ionic strength of the sample in orderto promote better electro-kinetic injection. In another example, thereagent carrier houses an internal lane standard (ILS). The ILS can beused for accurate size measurements. The reagent carrier also houses apolymer solution for electrophoretic separation in the micro-scale chipenvironment. The polymer solution is used as gels to provide a physicalseparation of DNA fragments according to chain length. For example, thepolymer solution can include a sieving or non-sieving matrix, such asthat disclosed in U.S. Pat. No. 7,531,073, No. 7,399,396, No. 7,371,533,No. 7,026,414, No. 6,811,977 and No. 6,455,682, which are incorporatedherein by reference in their entirety. In an example, a polymer sievingmatrix can be used to yield a single-base resolution in a totalseparation length of 8 cm and in less than 400 seconds.

The thermal module 120 receives control signals from the controllermodule 180, and induces suitable temperatures for DNA analysis, such asa temperature for DNA extraction, thermal cycles for the PCRamplification, a temperature for electrophoretic separation, and thelike. In an example, the thermal module 120 includes a resistance heaterto control a temperature in the wells of the sample acceptor for the DNAextraction and purification. In another example, the thermal module 120includes another resistance heater to control a temperature at thesecond domain 111 b.

In another example, the thermal module 120 includes a heating unit, acooling unit and a sensing unit to induce the thermal cycles for the PCRamplification at the first domain 111 a. The heating unit can directheat to the first domain 111 a, the cooling unit can disperse heat fromthe first domain 111 a, and the sensing unit can measure a temperatureat the first domain 111 a. The controller module 180 can control theheating unit and the cooling unit based on the temperature measured bythe sensing unit.

In an embodiment, the thermal module 120 performs non-contact thermalcontrols. For example, the thermal module 120 includes an infrared lightsource as the heating unit, a cooling fan as the cooling unit, and aninfrared pyrometer as the temperature sensing unit. The infrared lightsource, such as a halogen light bulb, can excite, for example, the 1.3μm vibrational band of liquid. Thus, the infrared light source can heata small volume of solution within a reservoir in the first domain 111 aindependent of the reservoir to achieve rapid heating and cooling. Theinfrared pyrometer measures blackbody radiation from an outside of thereservoir. In an example, the reservoir is designed to have a thinnerside for the infrared pyrometer measurements. The infrared pyrometermeasurements at the thinner side can more accurately reflect thetemperature of solution within the reservoir. Thus, the DNA analyzer 100can achieve a precise temperature control along with rapid thermalcycles. In an example, the DNA analyzer 100 can achieve a temperaturefluctuation of less than ±0.1° C., and a time of the thermal cycles forthe PCR amplification can be less than 20 minutes.

The pressure module 130 receives control signals from the controllermodule 180, and applies suitable pressures to the microfluidic chipmodule 110 to enable fluid movement. In an embodiment, the pressuremodule 130 receives a sensing signal that is indicative of a pressureapplied to the microfluidic chip module 110, and suitably adjusts itsoperation to maintain the suitable pressure to the microfluidic chipmodule 110.

The pressure module 130 can include a plurality of pumps. The pluralityof pumps control the injection of the various reagents and the templateDNA solutions into the microfluidic chip 111. According to an embodimentof the disclosure, the plurality of pumps can be individually controlledto achieve any possible timing sequence.

The pressure module 130 may include other pressure components to suitthe integrated single-chip integrated DNA analysis. In an embodiment,the microfluidic chip 111 has membrane valves. The pressure module 130can include a hydrodynamic pressure/vacuum system to suitably controlthe closing and opening of the membrane valves to enable fluid movementthrough the microfluidic chip 111.

In another embodiment, the microfluidic chip 111 is valveless. Forexample, the DNA analyzer 100 uses a liquid phase DNA extraction insteadof a silica solid phase DNA extraction. The liquid phase DNA extractioncan be integrated with following DNA processes on a valvelessmicrofluidic chip. Thus, the hydrodynamic pressure/vacuum system is notneeded. The pressure module 130 can be simplified to reduce thefootprint, the weight, the cost, and the complexity of the DNA analyzer100.

The power module 160 receives a main power, and generates variousoperation powers for various components of the DNA analyzer 100. In anexample, the DNA analyzer 100 is implemented using a modular design.Each module of the DNA analyzer 100 needs an operation power supply,which can be different from other modules. The power module 160 receivesan AC power input, such as 100-240 V, 50-60 Hz, single phase AC powerfrom a power outlet. Then, the power module 160 generates 5 V, 12 V, 24V, and the like, to provide operation powers for the various componentsof the DNA analyzer 100.

In addition, the power module 160 generates high voltages, such as 1000V, 2000 V, and the like, for suitable DNA processes on the microfluidicchip 111, such as electro-kinetic injection, electrophoretic separation,and the like.

Further, the power module 160 can implement various protectiontechniques, such as power outrage protection, graceful shut-down, andthe like, to protect the various components and data against powerfailure. It is noted that the power module 160 may include a back-uppower, such as a battery module, to support, for example, gracefulshut-down.

The high voltage module 140 can receive the high voltages from the powermodule 160 and suitably apply the high voltages on the microfluidic chip111. For example, the high voltage module 140 includes interfaces thatapply the high voltages to suitable electrodes on the microfluidic chip111 to induce electro-kinetic injection and/or electrophoreticseparation.

The detection module 150 includes components configured to suit theintegrated single-chip DNA analysis. In an embodiment, the detectionmodule 150 is configured for multicolor fluorescence detection. Thedetection module 150 includes a laser source unit, a set of optics and adetector unit.

The laser source unit emits a laser beam. In an example, the lasersource unit includes an argon-ion laser unit. In another example, thelaser source unit includes a solid state laser, such as a coherentsapphire optically pumped semiconductor laser unit. The solid statelaser has the advantages of reduced size, weight and power consumption.

The set of optics can direct the laser beam to pass through thedetection window at the second domain 111 b of the microfluidic chip111. The laser beam can excite fluorescent labels attached to DNAfragments to emit fluorescence. Further, the set of optics can collectand direct the emitted fluorescence to the detector unit for detection.In an STR typing example, STR alleles are separated in the second domain111 b according to sizes. STR alleles of different sizes pass thedetection window at different times. In addition, STR alleles ofoverlapping sizes can be tagged with fluorescent labels of differentcolors. The detector unit can be configured to detect an STR allelehaving a fluorescent label based on a time of fluorescence emitted bythe fluorescent label and a color of the emitted fluorescence.

In another example, internal lane standard (ILS) is added to migrate inthe micro channel with the STR alleles. The ILS includes DNA fragmentsof known sizes, and can be tagged with a pre-determined fluorescent dye.The detector unit detects fluorescence emitted from the ILS to set up asize scale. In addition, the detector unit detects fluorescence emittedfrom the STR alleles. The detector unit can suitably convert thedetected fluorescence into electrical signals. The electrical signalscan be suitably stored and/or analyzed. In an example, a processorexecutes DNA analysis software instructions to identify the STR allelesby their sizes and emitted fluorescence colors (wavelengths).

The computing module 170 includes computing and communication units. Inan example, the computing module 170 includes a personal computer. Thepersonal computer can be coupled with the controller module 180 toprovide a user interface. The user interface can inform the status ofthe DNA analyzer 100, and can receive user instructions for controllingthe operation of the DNA analyzer 100. The personal computer includesvarious storage media to store software instruction and data. Thepersonal computer can include DNA analysis software that can performdata processing based on raw data obtained from the detection module150. In addition, the personal computer can be coupled to externalprocessing units, such as a database, a server, and the like to furtherprocess the data obtained from the DNA analyzer 100.

The magnetic module 190 can enable a magnetic solid phase for theintegrated single chip DNA analysis. In an embodiment, the magneticsolid phase can be suitably incorporated in the integrated single chipDNA analysis to facilitate a volume reduction to suit for low copynumbers of template DNAs. In another embodiment, the magnetic solidphase can be suitably incorporated into an integrated single chipsequencing DNA analysis.

The controller module 180 can receive status signals and feedbacksignals from the various components, and provide control signals to thevarious components according to a control procedure. In addition, thecontroller module 180 can provide the status signals to, for example,the personal computer, to inform the user. Further, the controllermodule 180 can receive user instructions from the personal computer, andmay provide the control signals to the various components based on theuser instructions.

During operation, the controller module 180 receives user instructionsfrom the personal computer to perform a STR typing analysis, forexample. The controller module 180 then monitors the microfluidic chipmodule 110 to check whether a suitable disposable cartridge has beeninstalled, and whether swabs have been identified and suitably immersedin the liquid phase mixture to extract template DNA. When the controllermodule 180 confirms the proper status at the microfluidic chip module110, the controller module 180 starts a control procedure correspondingto the STR typing analysis. In an example, the controller module 180 cancontrol the thermal module 120 to maintain an appropriate temperature atthe wells of the sample acceptor for a predetermined time. The liquidphase mixture in the wells can extract template DNAs from the swabs.Then, the controller module 180 can control the pressure module 130 topump the extracted template DNAs into the first domain 111 a of themicrofluidic chip 111. In addition, the controller module 180 cancontrol the pressure module 130 to pump reagents for multiplexed STRamplification into the first domain 111 a.

Further, the controller module 180 can control the thermal module 120 toinduce thermal cycling for the multiplexed STR amplification at thefirst domain 111 a. The reagents and the thermal cycling can cause DNAamplification. In addition, the DNA amplicons can be suitably taggedwith fluorescent labels.

Subsequently, the controller module 180 can control the pressure module130 to flow the DNA amplicons to the second domain 111 b. The controllermodule 180 may control the pressure module 130 to pump a dilutionsolution into the microfluidic chip 111 to mix with the DNA amplicons.In addition, the controller module 180 may control the pressure module130 to pump an ILS into the microfluidic chip 111 to mix with the DNAamplicons.

Further, the controller module 180 controls the high voltage module 140to induce electro-kinetic injection to inject DNA fragments into themicro channels. The DNA fragments include the amplified targets, and theILS. Then, the controller module 180 controls the high voltage module140 to induce electrophoretic separation in the micro channels.Additionally, the controller module 180 can control the thermal module120 to maintain a suitable temperature at the second domain 111 b duringseparation, for example, to maintain the temperature for denaturingseparation of the DNA fragments.

The controller module 180 then controls the detection module 150 todetect the labeled DNA fragments. The detection module 150 can emit anddirect a laser beam to the micro channels to excite the fluorescentlabels to emit fluorescence. Further, the detection module 150 candetect the emitted fluorescence and store detection data in a memory.The detection data can include a detection time, and a detected color(wavelength), along with a detected intensity, such as a relativemagnitude of the detected fluorescence. The detection data can betransmitted to the personal computer for storage. Additionally, thecontroller module 180 can provide control statuses to the personalcomputer to inform the user. For example, the controller module 180 cansend an analysis completed status to the personal computer when thecontrol procedure is completed.

The DNA analyzer 100 can be suitably configured for various DNA analysesby suitably adjusting the reagents housed by the reagent carrier and thecontrol procedure executed by the controller module 180.

FIG. 2A shows a swab storage example 212, and FIGS. 2B-2C show a sideelevation view and a front elevation view of a sample cartridge example215 according to an embodiment of the disclosure. The swab storage 212includes a case 203, a seal cap 202 and a swab 205. The seal cap 202 andthe swab 205 are attached together. In addition, the swab storage 212includes an identifier, such as a barcode label 204 that can be attachedto the case 203, an RFID tag 201 that can be implanted in the seal cap202, and the like.

Before taking DNA sample, the swab 205 is safely stored in the case 203to avoid contamination. After taking DNA sample, the swab 205 can beplaced in the sample cartridge 215.

The sample cartridge 215 can include a microfluidic chip 211, a sampleacceptor 207 and a reagent carrier 206. The sample acceptor 207 includesa plurality of separated wells 207A-207D for taking swabs. Each wellincludes a liquid phase mixture 214 that is sealed by a membrane 208 ata bottom portion of the well. The liquid phase mixture 214 can conductenzymatic digestion of all proteins and other cellular interferences,with the exception of DNA, and thus can perform DNA extraction andpurification when a swab with DNA sample is inserted in the liquid phasemixture 214.

While the sample cartridge 215 is described in the context of swabs, itshould be understood that the sample cartridge 215 can be suitablyadjusted to suit other DNA gathering methods, such as blood stain cards,airborne samples, fingerprints samples, and the like.

In an embodiment, the seal cap 202 is a stepped seal cap that can sealthe well in a first step, and a second step. When the seal cap 202 sealsthe well in the first step, the swab 205 does not puncture the membrane208, and can be safely sealed in the well to maintain sample integrity.When the seal cap 202 seals the well in the second step, the swab 205punctures the membrane 208 and is immersed in the liquid phase mixture214.

The reagent carrier 206 houses various solutions for DNA analysis. In anSTR typing example, the reagent carrier houses reagents for multiplexedSTR amplification. In addition, the reagent carrier houses a coatingsolution, such as poly-N-hydroxyethylacrylamide, and the like. Thecoating solution can be used to coat micro channel walls prior to theseparation. Further, the reagent carrier houses a dilution solution,such as water, formamide, and the like. The dilution solution can beused to reduce the ionic strength in order to promote betterelectro-kinetic injection. In an embodiment, the reagent carrier housesan internal lane standard (ILS). The ILS can be used for sizemeasurement. The reagent carrier also houses a polymer solution forelectrophoretic separation in the micro-scale chip environment.

During operation, for example, a new disposable cartridge 215 is takenfrom a storage package, and installed in a DNA analyzer, such as the DNAanalyzer 100. Then, a swab 205 can be used to take a DNA sample. Theswab 205 is then identified and inserted into one of the wells 207A-207Dand sealed in the first step. Additional swabs 205 can be used to takeDNA samples, and then identified and inserted into the un-used wells207A-207D. Further, the DNA analyzer 100 can include a mechanism thatcan push the seal caps 202 to seal the wells 207A-207D in the secondstep, thus the swabs 205 can puncture the membrane 208, and immerse inthe liquid phase mixture 214.

FIG. 3 shows a schematic diagram of a microfluidic chip example 311according to an embodiment of the disclosure. The microfluidic chip 311includes various micro structures, such as inlets 312-314, reactionreservoirs 315-316, channels 317 a-317 b, electrode reservoirs 318,outlets (not shown), and the like, that are integrated for single-chipDNA analysis. It is noted that the various micro structures can bedesigned and integrated to suit for various DNA analyses, such as STRtyping, sequencing, and the like.

The inlets 312-314 can be coupled to a pressure module to injectsolutions in the microfluidic chip 311. As described above, theconnection can be made via a micro-macro interface. In an example, theinlet 312 is for injecting a template DNA solution from a well of thesample acceptor 207, and the inlet 313 is for injecting PCR reagentsfrom the reagent carrier 206. In addition, the inlet 313 can be used forinjecting dilution solution and ILS from the reagent carrier 206.

The reaction reservoirs 315-316 are configured for various purposes. Inan example, the reaction reservoir 315 is configured for the PCRamplification, and the reaction reservoir 316 is configured for thepost-PCR processes, such as dilution, and the like. More specifically,the reaction reservoir 315 is located in a first domain 311 a, which isa thermal control domain. The temperature within the thermal controldomain 311 a can be precisely controlled. In an example, an infraredheating unit directs heat to the thermal control domain 311 a, a coolingfan disperses heat from the thermal control domain 311 a, and aninfrared sensing unit measures a temperature in the thermal controldomain 311 a. The infrared heating unit and the cooling fan can becontrolled based on the temperature measured by the infrared sensingunit. The infrared heating unit, the cooling fan, and the infraredsensing unit can perform thermal control without contacting the thermalcontrol domain 311 a.

In another example, the temperature in the thermal control domain 311 ais measured by a thermal coupling technique. More specifically, themicrofluidic chip 311 includes a thermal-coupler reservoir 319 withinthe first domain 311 a. Thus, the solution temperature within thereaction reservoir 315 and the thermal-coupler reservoir 319 can beclosely related. The solution temperature within the thermal-couplerreservoir 319 can be measured by any suitable technique. Based on themeasured solution temperature within the thermal-coupler reservoir 319,the solution temperature within the reaction reservoir 315 can bedetermined. Then, the infrared heating unit and the cooling fan can becontrolled based on the temperature measured by the thermal couplingtechnique in order to control the solution temperature in the reactionreservoir 315.

In an embodiment, after the PCR amplification, the PCR mixture isfluidically directed from the reaction reservoir 315 to a post-PCRclean-up/dilution domain, such as the reaction reservoir 316. In thereaction reservoir 316, the PCR mixture is diluted. In an example, thePCR mixture and a dilutant solution are mixed together according to aratio from 1:5 to 1:20 (1 part of PCR mixture to 5-20 parts ofdilutant). Further, ILS can be added in the reaction reservoir 316 tomix with the PCR mixture.

The channels 317 a-317 b are located in a second domain 311 b. Electricfields can be suitably applied onto the channels 317 a-317 b. In anexample, the channels 317 a-317 b are configured according to a cross-Tdesign, having a short channel 317 a and a long channel 317 b.

The electrode reservoirs 318 can be used to apply suitable electricfields over the short channel 317 a and the long channel 317 b. Thus,the short channel 317 a is configured for electro-kinetic injection, andthe long channel 317 b is configured for electrophoretic separation. Forexample, when a high voltage is applied to the short channel 317 a, DNAfragments can be injected from the reaction reservoir 316 into the shortchannel 317 a at the intersection of the short channel 317 a and thelong channel 317 b. The long channel 317 b can be filed with sievingmatrix. When a high voltage is applied to the long channel 317 b, theinjected DNA fragments can migrate in the long channel 317 b to thepositive side of the electric field induced by the high voltage, in thepresence of the sieving matrix. In an example, the length of the longchannel 317 b is about 8.8 cm with detection at about 8 cm from theintersection.

It should be understood that the microfluidic chip 311 can include otherstructures to assist DNA analysis. In an example, the microfluidic chip311 includes an alignment mark 321. The alignment mark 321 can assist adetection module to align to the long channel 317 b.

During operation, for example, the inlet 312 can input a template DNAinto the reaction reservoir 315, and the inlet 313 can input PCRreagents into the reaction reservoir 315. Then, thermal-cycling can beinduced at the first domain 311 a, and PCR amplification can beconducted in the reaction reservoir 315 to amplify DNA fragments basedon the template DNA and the PCR reagents. After the PCR amplification,the DNA amplicons in the reaction reservoir 315 can be mobilized intothe reaction reservoir 316 in a liquid flow. In the reaction reservoir316, a dilution solution and ILS can be input to mix with the DNAfragments. Further, the DNA fragments in the reaction reservoir 316 canbe injected across the short channel 317 a by electro-kinetic injection.The DNA fragments then migrate in the long channel 317 b under the forceof electric field applied over the long channel 317 b. The speed ofmigration depends on the sizes of the DNA amplicons, in the presence ofthe sieving matrix. Thus, the DNA fragments are separated in the longchannel 317 b according to their sizes.

FIG. 4 shows an exemplary DNA analyzer 400 according to an embodiment ofthe disclosure. The DNA analyzer 400 is packaged in a box. The boxincludes handles, wheels and the like, to facilitate transportation ofthe DNA analyzer 400. In an implementation, the total weight of the DNAanalyzer 400 is less than 70 lb, and is appropriate for two persons tocarry.

The DNA analyzer 400 is implemented in a modular manner. Each module canbe individually packaged, and can include an interface for inter-modulecouplings. Thus, each module can be easily removed and replaced. Themodular design can facilitate assembly, troubleshooting, repair, and thelike.

The DNA analyzer 400 includes a user module (UM) 410, an active pressuremodule (APM) 430, a detection module 450, a power module (PM) 460, acomputing module 470, and a controller module (CM) 480. In addition, theDNA analyzer 400 includes a sample cartridge storage 415 and a swabstorage 412.

The UM 410 includes a holder to hold a sample cartridge, such as thesample cartridge 215, at an appropriate position when the samplecartridge is inserted by a user. Further, the UM 410 includes interfacecomponents to couple the sample cartridge 215 with, for example, the APM430, the detection module 450, and the like. The UM 410 includes thermalcomponents, such as resistance heaters 421, a cooling fan 422, aninfrared heating unit 423, and the like. The thermal components can besuitably positioned corresponding to the sample cartridge 215. Forexample, a resistance heater 421 is situated at a position that caneffectively control a temperature of the liquid phase mixture within theplurality of separated wells on the sample cartridge 215. Thetemperature can be determined to optimize enzyme activities of theliquid phase mixture to conduct enzymatic digestion of all proteins andother cellular interferences, with the exception of DNA. Anotherresistance heater 421 is at a position that can effectively control atemperature of the separation channel on the microfluidic chip 211. Theinfrared heating unit is at a position that can direct heat to thethermal control domain of the microfluidic chip 211 on the samplecartridge 215. The cooling fan is at a position that can effectivelydisperse heat from the thermal control domain. Further, the UM 410includes a high voltage module that can apply suitable high voltages viathe electrode reservoirs of the microfluidic chip 211.

It is noted that the UM 410 can include other suitable components. In anembodiment, the UM 410 includes a magnetic module that can suitablyapply magnetic control over a domain of the microfluidic chip 211.

The APM 430 includes suitably components, such as pumps, vacuums, andthe like, to apply suitable pressures to the microfluidic chip 211 toenable fluid movement.

The PM 460 receives an input main power, and generates various operationpowers, such as 6 V, 12 V, 24 V, 1000V, 2000V, and the like, for variouscomponents of the DNA analyzer 400.

The detection module 450 can include a laser module (LM) 451, a passiveoptics module (POM) 452, and an active optics module (AOM) 453. The LM451 can include any suitable device to emit a laser beam. In anembodiment, the LM 451 includes an argon-ion laser. In another example,the LM 451 includes a diode laser. In another embodiment, the LM 451includes a solid state laser, such as a coherent sapphire opticallypumped semiconductor laser. The solid state laser can have a reducedsize and weight, and can consume less power than the argon-ion laser. Inaddition, the solid state laser generates less waste heat, such that fansize can be reduced to reduce footprint of the DNA analyzer 400.

The AOM 453 includes optical elements that may need to be adjusted withregard to each inserted microfluidic chip. In an example, the AOM 453includes a plurality of optical fibers that are respectively coupled toa plurality of separation channels on the microfluidic chip. Theplurality of optical fibers can respectively provide laser beams to theplurality of separation channels to excite fluorescence emission. Inaddition, the plurality of optical fibers can return the emittedfluorescence from the plurality of separation channels.

The POM 452 includes various optical elements, such as lens, splitters,photo-detectors, and the like, that do not need to be adjusted withregard to each inserted microfluidic chip. In an example, the POM 452 iscalibrated and adjusted with regard to the LM 451 and the AOM 453 whenthe detection module 450 is assembled. Then, the optical elements withinthe POM 452 are situated at relatively fixed positions, and do not needto be adjusted with regard to each inserted microfluidic chip.

The controller module 480 is coupled to the various components of theDNA analyzer 400 to provide control signals for DNA analysis. Thecontroller module 480 includes a control procedure that determinessequences and timings of the control signals.

The computing module 470 is implemented as a personal computer. Thepersonal computer includes a processor, a memory storing suitablesoftware, a keyboard, a display, and a communication interface. Thecomputing module 470 can provide a user interface to ease user controland monitor of the DNA analysis by the DNA analyzer 400.

FIG. 5 shows a schematic diagram of a multiple-sample microfluidic chipexample 500 according to an embodiment of the disclosure. Themultiple-sample microfluidic chip 500 can be used to simultaneouslyperform DNA analysis for multiple samples. Similar to the microfluidicchip 311 in FIG. 3, the multiple-sample microfluidic chip 500 includesvarious micro structures, such as inlets 521-524, reaction reservoirs552, 562 and 572, connection channels 551,561, 571, 581, 553, 563 and573, injection channels 554, 564, 574 and 584, separation channels 555,565, 575 and 585, electrode reservoirs 531-540, waste reservoirs 524 and525, and the like. These micro structures can be similarly configured astheir corresponding micro structures in FIG. 3 and can operate similarlyas their corresponding micro structures in FIG. 3.

In addition, similar to the microfluidic chip 311, the multiple-samplemicrofluidic chip 500 includes a first domain 511 a, and a second domain511 b. The first domain 511 a is a thermal control domain, and thetemperature within the first domain 511 a can be controlled in a similarmanner as the thermal control domain 311 a.

The first domain 511 a can include multiple reaction reservoirs that arerespectively designated to multiple samples to perform simultaneous PCRamplification for the multiple samples. In the FIG. 5 example, thereaction reservoirs 552, 562 and 572 are located within the first domain511 a. During a PCR amplification step, for example, the reactionreservoir 552 includes a first liquid mixture of a first template DNAextracted from a first sample and first reagents, the reaction reservoir562 includes a second liquid mixture of a second template DNA extractedfrom a second sample and second reagents, and the reaction reservoir 572includes a third liquid mixture of a third template DNA extracted from athird sample and third reagents. Then, when thermal cycles are generatedwithin the first domain 511 a, for example, by an infrared light sourceand a cooling fan, PCR amplifications can be simultaneously performed inthe reaction reservoirs 552, 562 and 572.

In an embodiment, the first domain 511 a includes a thermal couplerreservoir (not shown) for measuring a temperature within the firstdomain 511 a. In another embodiment, the temperature measurement isperformed by an infrared sensing unit.

The second domain 511 b includes multiple separation units that arerespectively designated to multiple samples. In an embodiment, eachseparation unit includes a separation channel and an injection channelcoupled together. In addition, the separation unit includes electrodereservoirs that are in association with the injection channel and theseparation channel to provide electric fields for electro-kineticinjection and electrophoretic separation. It is noted that separationunits may share electrode reservoirs. In the FIG. 5 example, the seconddomain 511 b includes four separation units. The first separation unitincludes the injection channel 554 and the separation channel 555. Thesecond separation unit includes the injection channel 564 and theseparation channel 565. The third separation unit includes the injectionchannel 574 and the separation channel 575. The fourth separation unitincludes the injection channel 584 and the separation channel 585.

It is noted that the multiple-sample microfluidic chip 500 can includeother domains, such as post-PCR clean-up/dilution domain, and the like.Alternatively, a domain can be configured to be a multi-purpose domain.For example, the first domain 511 a can be suitably configured forpurification and/or post-PCR processing. Thus, the reaction reservoirs552, 562 and 572 can also be purification reservoirs and/or post-PCRreservoirs.

In another example, the electrode reservoirs 531, 533 and 536 aresuitably configured for diluting PCR mixtures. Specifically, theelectrode reservoir 531 dilutes a first PCR mixture received from thereaction reservoir 552 with a first dilutant, and prepares the first PCRmixture for electrophoretic separation in the separation channel 555.The electrode reservoir 533 dilutes a second PCR mixture received fromthe reaction reservoir 562 with a second dilutant, and prepares thesecond PCR mixture for electrophoretic separation in the separationchannel 565. The electrode reservoir 536 dilutes a third PCR mixturereceived from the reaction reservoir 572 with a third dilutant, andprepares the third PCR mixture for electrophoretic separation in theseparation channel 575. In an embodiment, respective dilution ratios areused in the electrode reservoirs 531, 533 and 536. The dilution ratiosare from 1:5 to 1:20 (one part of PCR mixture to 5-20 parts ofdilutant).

The various micro structures can be suitably coupled together to formmultiple processing units for multiple-sample DNA analysis. In FIG. 5example, the multiple-sample microfluidic chip 500 includes fourprocessing units. The first processing unit includes the inlets 521, theconnection channel 551, the reaction reservoir 552, the connectionchannel 553, the injection channel 554, and the separation channel 555.The second processing unit includes the inlets 522, the connectionchannel 561, the reaction reservoir 562, the connection channel 563, theinjection channel 564, and the separation channel 565. The thirdprocessing unit includes the inlets 523, the connection channel 571, thereaction reservoir 572, the connection channel 573, the injectionchannel 574, and the separation channel 575. The fourth processing unitincludes the inlet 524, the connection channel 581, the injectionchannel 584, and the separation channel 585.

The micro structures of a processing unit can be fluidically coupledtogether to enable liquid flow. Using the first processing unit as anexample, the inlets 521 are suitably coupled to a pump module. The pumpmodule can input the first template DNA and the first reagents into thereaction reservoir 552 via the connection channel 551 by a pressureforce. In the reaction reservoir 552, PCR amplification is performedbased on the first template DNA and the first reagents. After the PCRamplification, the DNA amplicons flow through the connection channel 553by a pressure force. Further, the DNA amplicons are injected into theseparation channel 555 via the injection channel 554 by anelectro-kinetic force. Then, electrophoretic separation can be performedin the separation channel 555.

The multiple processing units can be configured to fluidically separatedfrom each other on the same multiple-sample microfluidic chip 500. Thus,the multiple processing units can be respectively used to perform DNAanalysis for multiple samples using a single microfluidic chip.

It is noted that the processing units can be suitably configured toinclude branches. The branches can be suitably enabled or disabled.Using the first processing unit in FIG. 5 as an example, in addition tothe connection channel 553, the reaction reservoir 552 is also coupledto a connection channel 556 directing to the waste reservoir 524. In anembodiment, the connection channel 553 has a higher resistance than theconnection channel 556, for example, by having a smaller cross-sectionarea than the connection channel 556. However, the connection channel556 includes a valve 557. When the valve 557 is closed, the connectionchannel 556 is closed, then liquid can be forced to the higherresistance connection channel 553. When the valve 557 is open, liquidcan flow through the connection channel 556 to the waste reservoir 524.

It is also noted that the four processing units can be configured in asame manner or can be configured in different manners. In the FIG. 5example, the first, second and third processing units are configured ina same manner, and the fourth processing unit is configured differentlyfrom the other processing units. For example, each of the first, secondand third processing units includes a reaction reservoir in the firstdomain 511 a. In addition, corresponding connection channels, such asthe connection channels 553, 563 and 573, are suitably routed, such aszigzagged, to have substantially the same length. Thus, the first,second and third processing units can be used to perform DNA analysisfor three samples simultaneously. The fourth processing unit does notinclude a reaction reservoir in the first domain 511 a. Thus, the fourthprocessing unit can be used to perform DNA analysis for a sample thatdoes not need PCR amplification, or the PCR amplification for the sampleis suitably performed previously.

It is also noted that a multiple-sample microfluidic chip can includemultiple first domains, and/or second domains. In an example, amultiple-sample microfluidic chip may suitably include four sets of theschematic diagram in FIG. 5. Then, the multiple-sample microfluidic chipcan be used to simultaneously perform DNA analysis for twelve samples,or can be used to simultaneously perform electrophoretic separation forsixteen samples.

Of course, a multiple-sample microfluidic chip can be configured torepeat the structure in a single sample microfluidic chip, such as themicrofluidic chip 311. The repeated structures may be coupled together,or may be independent of each other. In an example, two structures arethermally coupled together. For example, the PCR reaction reservoirs ofthe two structures are thermally coupled together. In another example,two structures are fluidically coupled together. For example, the twostructures share a same inlet. In another example, the repeatedstructures are independent of each other. For example, the PCR reactionreservoirs of the repeated structures are thermally isolated, thusthermal cycles can be independently induced for the PCR reactionreservoirs.

Accordingly, a DNA analyzer can be suitably configured formultiple-sample DNA analysis. For example, a thermal module of the DNAanalyzer has a capability to generate thermal cycles within multiplefirst domains on a multiple-sample microfluidic chip, and the thermalmodule can be suitably configured to suit a multiple-sample microfluidicchip in use. In an embodiment, a thermal module of the DNA analyzerincludes a halogen light bulb to direct heat to a first domain, such asthe first domain 511 a, including multiple thermally coupled reactionreservoirs for PCR amplification. In another embodiment, a thermalmodule of the DNA analyzer includes multiple heat sources that canindependently direct heat to thermally isolated reaction reservoirs. Inanother example, a detection module of the DNA analyzer has a capabilityto detect fluorescence from sixteen separation channels. The detectionmodule can be suitably configured to suit a multiple-sample microfluidicchip in use.

FIG. 6 shows a block diagram of a detection module example 650 coupledwith a multiple-sample microfluidic chip example 611 for multiple-sampleDNA analysis according to an embodiment of the disclosure. Themultiple-sample microfluidic chip 611 is similarly configured as themultiple-sample microfluidic chip 511 to include four separationchannels. During an operation, for example, the four separation channelsare used to simultaneously perform electrophoretic separation for foursamples. The detection module 650 has a capability of detectingfluorescence from sixteen separation channels, and can be suitablyconfigured according to the multiple-sample microfluidic chip 611 inuse.

The detection module 650 includes a laser module 651, a passive opticsmodule 652 and an active optics module 653. These elements can becoupled together as shown in FIG. 6. In an embodiment, the detectionmodule 650 is implemented according to modular design. Each of the lasermodule 651, the passive optics module 652 and the active optics module653 can be individually handled, such as manufactured, purchased,tested, and calibrated. Further, the laser module 651, the passiveoptics module 652 and the active optics module 653 can be suitablycoupled together, and assembled in a DNA analyzer.

In an example, these modules can be coupled together by optical fibers.The laser module 651 generates a laser beam. The laser beam is providedto the passive optics module 652 via an optical fiber 671. The passiveoptics module 652 has a capability to split the laser beam into sixteenlaser beams. The sixteen laser beams are provided to the active opticsmodule 653 via sixteen optical fibers 673. The active optics module 653has a capability to respectively focus the sixteen laser beams ontosixteen separation channels, respectively collect fluorescence from thesixteen separation channels and return the collected fluorescence to thepassive optics module 652 via the sixteen optical fibers 673. Thepassive optics module 652 can include detectors to convert opticalsignals, such as the returned fluorescence, into electrical signals. Theelectrical signals can then be suitably stored and processed.

More specifically, the laser module 651 can include any suitably laserdevice, such as an argon-ion laser device, a solid state laser, and thelike, to generate the laser beam. In an example, the laser module 651includes a coherent sapphire optically pumped semiconductor laser (OPSL)outputs a laser beam of 488 nm wavelength, and has an output power of200 mW.

The passive optics module 652 can use any suitable techniques to splitthe received laser beam into the sixteen laser beams. In the FIG. 6example, the passive optics module 652 splits the laser beam by twostages. In a first stage, the passive optics module 652 uses a splitter661 to split the laser beam into four sub-laser beams. In a secondstage, the passive optics module 652 uses four splitter/MUX units 662 torespectively split the four sub-laser beams into the sixteen laserbeams. The sixteen laser beams are feed to the active optics module 653by the sixteen optical fibers 673.

The active optics module 653 includes sixteen focus units 654, such asobjective lenses, that can respectively focus the sixteen laser beams tosixteen separation channels. In addition, each objective lens cancollect and return fluorescence excited by the laser beam. The activeoptics module 653 can include a motor, such as a micro-piezo steppermotor, that can be coupled to the focus units 654 to align the focusunits 654 to separation channels.

In the FIG. 6 example, when the multiple-sample microfluidic chip 611uses four separation channels during operation, the active optics module653 selectively align four of the focus units 654 to the four separationchannels. The other focus units 654 may be suitably disabled.

The returned fluorescence can be transmitted to the passive opticsmodule 652 via the sixteen optical fibers 673. The passive optics module652 can include one or more detectors to detect properties, such aswavelength, intensity, timings, and the like, of the excitedfluorescence from the sixteen separation channels.

In the FIG. 6 example, the passive optics module 652 uses the foursplitter/MUX units 662 to multiplex the optical signals from the sixteenoptical fibers 673 into four multiplexed optical signals 675. Further,the passive optics module 652 uses four signal processing units torespectively process the four multiplexed optical signal 675. In anexample, each signal processing unit includes a filter 663, such asacousto optic tunable filter (AOTF), and a photo-detector 664, such asavalanche photo detector (APD), coupled together. The filter 663 filtersthe optical signal 675 based on wavelengths. More specifically, thefilter 663 passes a portion of the optical signal 675 having a tunablewavelength, and blocks the rest of the optical signal 675. Then, thephoto-detector 663 generates an electrical signal in response to thefiltered optical signal. The electrical signal can be suitablyprocessed, such as spectrally separated, phase-demodulated, digitalized,and stored. In the FIG. 6 example, the passive optics module 652includes a data connector interface 665 to transmit the digitalized datato another module, such as a computer module, for post-processing.

FIG. 7 shows a flow chart outlining an exemplary process for using a DNAanalyzer, such as the DNA analyzer 400, to perform multiple-sample DNAanalysis according to an embodiment of the disclosure. The processstarts at S701, and proceeds to S710.

At S710, a user of the DNA analyzer 400 plugs in a main power supply. Inan embodiment, the main power supply can be a 110 V, 50 Hz, AC powersupply, or can be a 220V, 60 Hz, AC power supply. The power module 460can convert the main power supply to a plurality of operation powers,and provide the plurality of operation powers to the various modules ofthe DNA analyzer 400. Then, the process proceeds to S715.

At S715, the user starts up a user control interface. For example, theuser turns on the personal computer 470, and starts a software packagethat interacts with the user and the controller module 480. The softwarepackage enables the personal computer 470 to provide a user controlinterface on the display. Further, the software package enables thepersonal computer 470 to receive user instructions via keyboard ormouse. The software packages can also enable the personal computer 470to communicate with the controller module 480. Then, the processproceeds to S720.

At S720, the user instructs the DNA analyzer 400 to initialize. The usercontrol interface receives the initialization instruction, and thesoftware package enables the personal computer 470 to send theinitialization instruction to the controller module 480. The controllermodule 480 can then initialize the various components of the DNAanalyzer 400. The controller module 480 can power on the variouscomponents, check the status and reset the status if needed. Then, theprocess proceeds to S725.

At S725, the user inserts a sample cartridge, such as the samplecartridge 215, in the UM 410. The sample cartridge 215 includes amultiple-sample microfluidic chip, such as the multiple-samplemicrofluidic chip 500. In addition, the sample cartridge 215 includes asample acceptor having multiple wells to respectively accept multiplesamples. The sample cartridge 215 can be positioned by a holder. Theinterface components can suitably couple the sample cartridge 215 to theother components of the DNA analyzer 400. Then, the process proceeds toS730.

At S730, the user takes a swab 205, and lets the DNA analyzer 400 toidentify the swab 205. In an example, the DNA analyzer 400 includes abarcode reader that can read the barcode label 204 attached to the case203 for storing the swab 205. In another example, the DNA analyzer 400excites the RFID 201 implanted in the seal cap 202 of the swab 205 toobtain a unique serial number of the swab 205. Then, the processproceeds to S735.

At S735, the user uses the swab 205 to take a DNA sample and inserts theswab 205 into a well of the sample cartridge 215. Then, the processproceeds to S736.

At S736, the user determines whether to insert more samples. When thesample cartridge can take more samples and more samples are available,the process returns to S730 for the user to insert more samples in thesample cartridge 215. When the sample cartridge is full or no moresample is available, the process proceeds to S740.

At S740, the user instructs the DNA analyzer 400 to start a DNAanalysis. The user control interface receives the start instruction, andthe software package enables the personal computer 470 to send the startinstruction to the controller module 480. The controller module 480 canstart a control procedure corresponding to the DNA analysis. In anexample, the controller module 480 starts an STR typing procedurecorresponding to a multiplexed STR typing analysis. In another example,the controller module 480 starts a sequencing procedure corresponding toDNA sequencing analysis. In an embodiment, the control procedure startswith an alignment instruction. The alignment instruction can be sent tosuitable components to align the components to suit for multiple-sampleDNA analysis. For example, the alignment instruction is sent to adetection module, such as the detection module 650. The detection module650 is then suitably initialized according to, for example, theconfiguration of the multiple-sample microfluidic chip 500, a number ofsamples being inserted, and the like. Then, the process proceeds toS745.

At S745, the user waits and monitors the status of the DNA analysis. Thecontrol procedure can specify sequences and timings of control signalsto various components of the DNA analyzer 400 corresponding to themultiple-sample DNA analysis. Then, the controller module 480automatically sends the control signals according to the sequences andthe timings in the control procedure. In addition, the controller module480 receives status and feedback signals from the various components,and sends them to the personal computer 470. The personal computer 470then provides the analysis status for the user to monitor. Then, theprocess proceeds to S750.

At S750, the controller module 480 finishes executing the controlprocedure, and sends an analysis-completed status to the personalcomputer 470. The personal computer 470 can inform the user of theanalysis-completed status via the user control interface. Then, theprocess proceeds to S755.

At S755, the user performs post data processing. The user can store theraw data of the DNA analysis, or transmit the raw data to a remotereceiver. In addition, the user may start a software package for postdata processing. Alternatively, the software package for post dataprocessing can be suitably integrated with the control procedure. Thus,after the control procedure is successfully executed, the softwarepackage for post data processing is executed automatically to performpost data processing. The process then proceeds to S799 and terminates.

It is noted that to perform another DNA analysis, the user may throwaway the sample cartridge and repeat S720-S750. It is also noted thatthe sequence of the DNA analysis steps can be suitably adjusted. Forexample, S735 and S730 can be swapped, thus a swab can be first used totake a DNA sample, and then identified by the DNA analyzer 400.

FIG. 8 shows a flow chart outlining an exemplary process for a DNAanalyzer to perform a multiple-sample DNA analysis according to anembodiment of the disclosure. The DNA analyzer includes amultiple-sample microfluidic chip, such as the multiple-samplemicrofluidic chip 500. The multiple-sample microfluidic chip includesmultiple processing units for processing multiple samples respectively.Each processing unit includes its respective inlets, connectionchannels, a reaction reservoir in a thermal control domain, an injectionchannel and a separation channel coupled together. The process starts atS801 and proceeds to S805.

At S805, the controller module 480 sends alignment instructions tomodules in the DNA analyzer to align in response to inserted multiplesamples. In an example, three samples are inserted in a sample acceptorfor simultaneous DNA analysis. The controller module 480 determinesthree processing units for the simultaneous DNA analysis. In addition,the controller 480 sends the alignment instructions to, for example, theAPM 430 to align pumps to inlets of the three processing units, theUM410 to align high voltage sources to electro reservoirs of the threeprocessing units, and the detection module 450 to align objective lensesto separation channels of the three processing units. Then, the processproceeds to S810.

At S810, the controller module 480 controls the resistance heater 421 tomaintain a temperature for extraction and purification of template DNAfrom the multiple samples. In an example, the resistance heater 421 ispositioned corresponding to multiple wells on the sample cartridge 215.The multiple wells accept multiple DNA samples, such as multiple swabs205 used to take DNA sample. In an example, the multiple swabs 205 areforced to respectively puncture membranes that seal a liquid phasemixture at the bottom of the their respective wells, thus the multipleswabs 205 are respectively immersed into the liquid phase mixture. Theliquid phase mixture can extract and purify template DNA from the swabat the temperature according to enzymatic DNA isolation method. In anembodiment, the liquid phase mixture can achieve a compatible DNAconcentration and purity to silica based solid phase extraction methodin about 6 minutes. Thus, multiple template DNAs can be extracted andpurified simultaneously. Then, the process proceeds to S820.

At S820, the controller module 480 controls the APM 430 to pump eachextracted template DNA and reagents into a processing unit on themultiple-sample microfluidic chip. In an STR typing example, the reagentcarrier 206 houses reagents for multiplexed STR amplification. Thecontroller module 480 sends control signals to the APM 430. In responseto the control signals, a pump module respectively pumps the multipleextracted template DNAs from the multiple wells into the multiplereaction reservoirs in the thermal control domain, and also pumps thereagents from the reagent carrier 206 into the multiple reactionreservoirs. Then, the process proceeds to S830.

At S830, the controller module 480 controls the cooling fan 422 and theinfrared heating unit 423 to induce thermal cycling in the thermalcontrol domain for the multiplexed STR amplification. In addition, thereagents can attach fluorescent labels to DNA during the STRamplification process. The process then proceeds to S840.

At S840, after the PCR amplification, the solution can be diluted. In anembodiment, the controller module 480 sends control signals to the APM430 after the PCR amplification. In response to the control signals, theAPM 430 respectively pumps a dilution solution into the multiplereaction reservoirs. The process then proceeds to S850.

At S850, the controller module 480 sends control signals to the highvoltage module in the UM 410 to respectively inject the DNA ampliconsacross the injection channels to the respectively separation channels.Then, the process proceeds to S860.

At S860, the controller module 480 sends control signals to the highvoltage module in the UM 410 to apply appropriate high voltage over themultiple separation channels of the multiple processing units toseparate the DNA amplicons based on size. The process then proceeds toS870.

At S870, the controller module 480 sends control signals to thedetection module 450 to excite and detect emitted fluorescence from themultiple separation channels. The raw detection data can be sent to thepersonal computer 470 for storage and post-processing. The process thenproceeds to S899, and terminates.

It is noted that some process steps in the process 800 can be executedin parallel. For example, the step S860 and the step S870 can beexecuted in parallel. The controller module 480 sends control signals toboth the high voltage module in the UM 410 and the detection module 450at about the same time. The control signals to the high voltage modulein the UM 410 cause the electrophoretic separation in the separationchannel, while the control signals to the detection module 450 causefluorescence detection.

While the invention has been described in conjunction with the specificexemplary embodiments thereof, it is evident that many alternatives,modifications, and variations will be apparent to those skilled in theart. Accordingly, exemplary embodiments of the invention as set forthherein are intended to be illustrative, not limiting. There are changesthat may be made without departing from the spirit and scope of theinvention.

1. A microfluidic chip, comprising: a first domain configured forpolymerase chain reaction (PCR) amplification of DNA fragments, thefirst domain including at least a first reaction reservoir designatedfor PCR amplification based on a first sample, and a second reactionreservoir designated for PCR amplification based on a second sample; anda second domain including at least a first separation unit coupled tothe first reaction reservoir to received first amplified DNA fragmentsbased on the first sample, and a second separation unit coupled to thesecond reaction reservoir to received second amplified DNA fragmentsbased on the second sample, the first separation unit being configuredto perform electrophoretic separation for the first amplified DNAfragments, and the second separation unit being configured to performelectrophoretic separation for the second amplified DNA fragments. 2.The microfluidic chip of claim 1, further comprising: first inletsconfigured to input a first template DNA extracted from the first sampleand first reagents for PCR amplification into the first reactionreservoir; and second inlets configured to input a second template DNAextracted from the second sample and second reagents for PCRamplification into the second reaction reservoir.
 3. The microfluidicchip of claim 1, wherein the first separation unit further comprises: afirst separation channel configured to separate the first amplified DNAfragments by electrophoretic separation; and a first injection channelconfigured to inject the first amplified DNA fragments into the firstseparation channel by electro-kinetic injection; and the secondseparation unit further comprises: a second separation channelconfigured to separate the second amplified DNA fragments byelectrophoretic separation; and a second injection channel configured toinject the second amplified DNA fragments into the second separationchannel by electro-kinetic injection.
 4. The microfluidic chip of claim1, wherein the first separation unit further comprises: first electrodereservoirs configured to apply electric fields for the electro-kineticinjection and the electrophoretic separation; and the second separationunit further comprises: second electrode reservoirs configured to applyelectric fields for the electro-kinetic injection and theelectrophoretic separation.
 5. The microfluidic chip of claim 4, whereinthe first separation unit and the second separation unit share at leastone electrode reservoir.
 6. The microfluidic chip of claim 1, whereinthe first domain further comprises: a thermal coupler reservoirconfigured for measuring a temperature within the first domain.
 7. Themicrofluidic chip of claim 1, further comprising: a dilution domainconfigured to dilute PCR mixtures received from the first domain andprepare the PCR mixtures for electrophoretic separations in the seconddomain, the dilution domain including a first dilution reservoirdesignated for diluting a first PCR mixture received from the firstreaction reservoir, and a second dilution reservoir designated fordiluting a second PCR mixture received from the second reactionreservoir.
 8. The microfluidic chip of claim 7, wherein the firstdilution reservoir dilutes the first PCR mixture with a first dilutantaccording to a first ratio from 1:5 to 1:20, and the second dilutionreservoir dilutes the second PCR mixture with a second dilutantaccording to a second ratio from 1:5 to 1:20.
 9. A DNA analyzer that isconfigured to receive and act on the microfluidic chip of claim 1 toperform DNA analysis.
 10. A cartridge, comprising: a sample acceptorconfigured to respectively extract a first template DNA from a firstsample and a second template DNA from a second sample; and amicrofluidic chip having a first domain configured for polymerase chainreaction (PCR) amplification of DNA fragments, the first domainincluding at least a first reaction reservoir designated for PCRamplification based on the first template DNA, and a second reactionreservoir designated for PCR amplification based on the second templateDNA; and a second domain including at least a first separation unitcoupled to the first reaction reservoir to received first amplified DNAfragments based on the first template DNA, and a second separation unitcoupled to the second reaction reservoir to received second amplifiedDNA fragments based on the second template DNA, the first separationunit being configured to perform electrophoretic separation for thefirst amplified DNA fragments, and the second separation unit beingconfigured to perform electrophoretic separation for the secondamplified DNA fragments.
 11. The cartridge of claim 10, furthercomprising: a reagent carrier configured to carry reagents for the PCRamplification, and solutions for the electrophoretic separation.
 12. Thecartridge of claim 10, wherein the sample acceptor is configured toextract the first template DNA or the second template DNA by at leastone of a solid phase extraction, and a liquid phase enzymatic DNAisolation.
 13. The cartridge of claim 10, wherein the sample acceptorcomprises a first well having a first liquid phase mixture to extractthe first template DNA from the first sample and a second well having asecond liquid phase mixture to extract the second template DNA from thesecond sample.
 14. The cartridge of claim 11, wherein the microfluidicchip further comprises: first inlets configured to input the firsttemplate DNA and first reagents for PCR amplification into the firstreaction reservoir; and second inlets configured to input the secondtemplate DNA and second reagents for PCR amplification into the secondreaction reservoir.
 15. The cartridge of claim 11, wherein the firstseparation unit of the microfluidic chip further comprises: a firstseparation channel configured to separate the first amplified DNAfragments by electrophoretic separation; and a first injection channelused for injecting the first amplified DNA fragments into the firstseparation channel by electro-kinetic injection; and the secondseparation unit of the microfluidic chip further comprises: a secondseparation channel configured to separate the second amplified DNAfragments of the second sample by electrophoretic separation; and asecond injection channel used for injecting the second amplified DNAfragments into the second separation channel by electro-kineticinjection.
 16. The cartridge of claim 15, wherein the first separationunit further comprises: first electrode reservoirs configured to applyelectric fields for the electro-kinetic injection and theelectrophoretic separation; and the second separation unit furthercomprises: second electrode reservoirs configured to apply electricfields for the electro-kinetic injection and the electrophoreticseparation.
 17. The cartridge of claim 16, wherein the first separationunit and the second separation unit share at least one electrodereservoir.
 18. The cartridge of claim 10, wherein the microfluidic chipfurther comprises: a dilution domain configured to dilute PCR mixturesreceived from the first domain and prepare the PCR mixtures forelectrophoretic separations in the second domain, the dilution domainincluding a first dilution reservoir designated for diluting a first PCRmixture received from the first reaction reservoir, and a seconddilution reservoir designated for diluting a second PCR mixture receivedfrom the second reaction reservoir.
 19. The cartridge of claim 10,wherein the first dilution reservoir dilutes the first PCR mixture witha first dilutant according to a first ratio from 1:5 to 1:20, and thesecond dilution reservoir dilutes the second PCR mixture with a seconddilutant according to a second ratio from 1:5 to 1:20.
 20. A method formultiple-sample DNA analysis, comprising: inducing thermal cycles in afirst domain of a microfluidic chip for PCR amplification of DNAfragments, the first domain including at least a first reactionreservoir designated for PCR amplification based on a first sample, anda second reaction reservoir designated for PCR amplification based on asecond sample; inducing liquid flow to respectively move first amplifiedDNA fragments from the first reaction reservoir to a first separationunit in a second domain of the microfluidic chip, and second amplifiedDNA fragments from the second reaction reservoir to a second separationunit in the second domain of the microfluidic chip; inducing electricfields in the first separation unit to separate the first amplified DNAfragments by size; inducing electric fields in the second separationunit to separate the second amplified DNA fragments by size; anddetecting the separated DNA fragments.
 21. The method of claim 20,further comprising: extracting a first template DNA from the firstsample; and extracting a second template DNA from the second sample. 22.The method of claim 21, further comprising: maintaining a temperature toenable liquid phase enzymatic DNA isolation for extracting at least oneof the first template DNA and the second template DNA.
 23. The method ofclaim 21, further comprising: injecting first reagents and the firsttemplate DNA into the first reaction reservoir; and injecting secondreagents and the second template DNA into the second reaction reservoir.24. The method of claim 20, wherein detecting the separated DNAfragments further comprises: emitting a laser beam; splitting the laserbeam into a first laser beam and a second laser beam; directing thefirst laser beam to a first separation channel of the first separationunit to excite a first fluorescence from first fluorescent labelsattached to the first amplified DNA fragments; directing the secondlaser beam to a second separation channel of the second separation unitto excite a second fluorescence from second fluorescent labels attachedto the second amplified DNA fragments; and detecting the firstfluorescence and the second fluorescence.
 25. The method of claim 24,wherein detecting the first fluorescence and the second fluorescencecomprises: detecting the first fluorescence by a first detector; anddetecting the second fluorescence by a second detector.
 26. The methodof claim 24, wherein detecting the first fluorescence and the secondfluorescence comprises: multiplexing the first fluorescence and thesecond fluorescence; and detecting the multiplexed fluorescence by adetector.
 27. The method of claim 20, wherein inducing liquid flow torespectively move the first amplified DNA fragments from the firstreaction reservoir to the first separation unit in the second domain ofthe microfluidic chip, and the second amplified DNA fragments from thesecond reaction reservoir to the second separation unit in the seconddomain of the microfluidic chip, further comprises: inducing liquid flowto move a first PCR mixture having the first amplified DNA fragmentsfrom the first reaction reservoir to a first dilution reservoir;diluting the first PCR mixture with a first dilutant; inducing liquidflow to move a second PCR mixture having the second amplified DNAfragments from the second reaction reservoir to a second dilutionreservoir; and diluting the second PCR mixture with a second dilutant.28. The method of claim 27, wherein diluting the first PCR mixture withthe first dilutant and diluting the second PCR mixture with the seconddilutant, further comprises: diluting the first PCR mixture with thefirst dilutant according to a first ratio from 1:5 to 1:20; and dilutingthe second PCR mixture with the second dilutant according to a secondratio from 1:5 to 1:20.